scholarly journals Genetic code as an image of the mirror image. Part I

2019 ◽  
Author(s):  
Miloje M. Rakočević
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Mirror Symmetry ◽  
Essential Feature ◽  
Mirror Image ◽  
Side Chains ◽  
Chemical Similarity ◽  
Protein Amino Acids ◽  
Image Part

The paper starts from the established facts about a system consisting of 20 protein amino acids (AAs), arranged according to a hierarchy of chemical similarity (Rakočević, 2019). There, it was shown that the number of atoms in the side chains of AAs given in the arrangement of 5 x 4 is such that it represents a mirror image in a specific way generated sequence of numbers: 02, 13, 24, 16, 05 (20, 31, 42, 61, 50 ). Further in the paper new insights have been preseted to show that mirror symmetry is in many respects an essential feature of the genetic code.

scholarly journals Genetic code as an image of the mirror image. Supplement 1

2019 ◽  
Author(s):  
Miloje M. Rakočević
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Binary Tree ◽  
Mirror Symmetry ◽  
Essential Feature ◽  
Binary Sequence ◽  
Number System ◽  
Mirror Image ◽  
Chemical Similarity ◽  
Decimal Number

Searching for the answer to the question why – in the generating of the genetic code – only mirror symmetrical left and not right amino acids (AAs) were selected, in a previous work we showed the existence of a double Boolean "triangle" in mirror symmetry, with superposition of the top vertices: 00 -11-22 / 22-11-00 → 00-11-22-11-00 [0 as 000; 1 as 001; 2 as 010] (Rakočević, 2019a). The resulting sequence, summed with the binary sequence of a 6-bit binary tree, split with a mirror in the middle (101/010) [as in Dirac's positron / electron mirror], results in a sequence of decimal number system: 02-13-24-16-05, where a smaller number (010 = 2) was added three times and a larger number (101 = 5) twice (Survey 1). The mirror image of the obtained decimal sequence (20-31-42-61-50) is 100% consistent with the arrangement of protein AAs, arranged according to strict chemical similarity (Rakočević, 2019a, Table 3). Starting from this result, the paper of which this is a supplement, presents new insights and new examples of mirror symmetry valid for the genetic code, showing that mirror symmetry is also in other respects an essential feature of the genetic code. In this Supplement are given the further new insights.

scholarly journals System-directed pairing of protein amino acids. Part II

2021 ◽  
Author(s):  
Miloje M. Rakočević
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Chemical Similarity ◽  
Protein Amino Acids

In this second part of the paper, the pairs of protein amino acids (AAs), canonical in the genetic code (GC) in the three system-arrangements (OS, DS and AS), presented in the first part, are compared with the Table of chemical similarity of AAs (Table 1 in Part I). The obtained results are such that it makes sense to speak about an ORiginal CHEmical STandard (Orchest), valid not only for amino acids but for life complete.

scholarly journals Making Sense of “Nonsense” and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications

2022 ◽  
Vol 23 (2) ◽  
pp. 938
Author(s):  
Olubodun Michael Lateef ◽  
Michael Olawale Akintubosun ◽  
Olamide Tosin Olaoba ◽  
Sunday Ocholi Samson ◽  
Malgorzata Adamczyk
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Protein Design ◽  
Side Chains ◽  
Vast Number ◽  
Trna Modifications ◽  
Wide Range ◽  
Challenges And Opportunities ◽  
Code Extension ◽  
Genetic Code Expansion

The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.

scholarly journals Genetic code: Chemical Distinctions of Protein Amino Acids

2017 ◽  
Author(s):  
Miloje M. Rakocevic
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Standard Genetic Code ◽  
Atom Number ◽  
Canonical Bases ◽  
Ordinal Numbers ◽  
Intelligent Structures ◽  
Protein Amino Acids

In the work it is shown that 20 protein amino acids ("the canonical amino acids" within the genetic code) appear to be a whole and very symmetrical system, in many ways, all based on strict chemical distinctions from the aspect of their similarity, complexity, stereochemical and diversity types. By this, all distinctions are accompanied by specific arithmetical and algebraic regularities, including the existence of amino acid ordinal numbers from 1 to 20. The classification of amino acids into two decades (1-10 and 11-20) appears to be in a strict correspondence with the atom number balances. From the presented "ideal" and "intelligent" structures and arrangements follow the conclusions that the genetic code was complete even in prebiotic conditions (as a set of 20 canonical amino acids and the set of 2+2 pyrimidine / purine canonical bases, respectively); and the notion "evolution" of the genetic code can only mean the degree of freedom of standard genetic code, i.e. the possible exceptions and deviations from the standard genetic code. [This is the second version with minimal interventions in the text. In addition, one passage was added in front of the second star, with quoting of T. Jukes. Added is Remark 4 and a more adequate shading in the Table inside Box 2.]

scholarly journals Genetic code as an image of the mirror image. Part II

2020 ◽  
Author(s):  
Miloje M. Rakočević
Keyword(s):  
Genetic Code ◽  
Mirror Image ◽  
Scientific Note ◽  
Image Part

This unifying paper represents a compilation of three small works, published in OSF Preprints. All three works are related to the first part of the paper entitled with the same title as this, they are practically its continuation. The reason for giving up writing a special text as "Part II" and declaring two supplements and one scientific note as "Part II" lies in the epilogue of the first part of this paper, which (epilogue) I give here in Appendix.

scholarly journals Genetic code research: a precognition result (II)

2021 ◽  
Author(s):  
Miloje M. Rakočević
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Short Communication ◽  
Number System ◽  
Multiplication Table ◽  
The Other ◽  
Decimal Number ◽  
Other Hand ◽  
Protein Amino Acids

In this second part of the short communication (Ref. 2), we give an argument more in favor of the validity of the precognition status of the final result of my 40 years of genetic code researches. It is shown that the changes in the number of atoms in the system-arrangements of protein amino acids, in relation to the Gaussian number (51) and the Dürer number (34 and 68, respectively), correspond to the changes in the products of number 5 in the Multiplication Table of the decimal number system. On the other hand, with the same changes (in the products of number 5), two unconscious narrations, said in the first part of this communication, correspond one hundred percent.

scholarly journals Engineering Pyrrolysyl-tRNA Synthetase for the Incorporation of Non-Canonical Amino Acids with Smaller Side Chains

2021 ◽  
Vol 22 (20) ◽  
pp. 11194
Author(s):  
Nikolaj G. Koch ◽  
Peter Goettig ◽  
Juri Rappsilber ◽  
Nediljko Budisa
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Cell Biology ◽  
Trna Synthetase ◽  
Side Chains ◽  
Site Specific ◽  
Biomaterial Science ◽  
Key Residues ◽  
Small Side

Site-specific incorporation of non-canonical amino acids (ncAAs) into proteins has emerged as a universal tool for systems bioengineering at the interface of chemistry, biology, and technology. The diversification of the repertoire of the genetic code has been achieved for amino acids with long and/or bulky side chains equipped with various bioorthogonal tags and useful spectral probes. Although ncAAs with relatively small side chains and similar properties are of great interest to biophysics, cell biology, and biomaterial science, they can rarely be incorporated into proteins. To address this gap, we report the engineering of PylRS variants capable of incorporating an entire library of aliphatic “small-tag” ncAAs. In particular, we performed mutational studies of a specific PylRS, designed to incorporate the shortest non-bulky ncAA (S-allyl-l-cysteine) possible to date and based on this knowledge incorporated aliphatic ncAA derivatives. In this way, we have not only increased the number of translationally active “small-tag” ncAAs, but also determined key residues responsible for maintaining orthogonality, while engineering the PylRS for these interesting substrates. Based on the known plasticity of PylRS toward different substrates, our approach further expands the reassignment capacities of this enzyme toward aliphatic amino acids with smaller side chains endowed with valuable functionalities.

scholarly journals System-directed pairing of protein amino acids. Part I

2021 ◽  
Author(s):  
Miloje M. Rakočević
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Chemical Reactions ◽  
Review Paper ◽  
Point Of View ◽  
Second Phase ◽  
Protein Amino Acids ◽  
The Moment ◽  
Current Science

The idea of this review paper is as follows. If it can be shown (and it can!) that the pairing of protein amino acids is system-directed (determined), then the hypothesis of a prebiotically determined genetic code (Rakočević, 2004a) gets its full meaning. The hypothesis is supported by the fact that all these pairings come to the fore primarily through classes and subclasses of amino acid molecules. What is, however, unexpected and even unbelievable from the point of view of current science is the fact that the quantities, i.e. number of atoms (in a direct or indirect relation to the number of nucleons), in these classes and subclasses, are determined by Gauss’ number 51 (51 = 3 x 17), or Gauss’ sequence: 51 ± 10, 51 ± 20, 51 ± 30, 51 ± 40 and 51 ± 50; also by Dürer’s number 34 (34 = 2 x 17), even more either by its double value, 68; or by Dürer’s sequences: 34 ± 10, 34 ± 5 and 68 ± 10, 68 ± 5. Since the hypothesis refers to constituents – amino acids and nucleotides – it follows that in terms of the type and number of constituents, it makes no sense to talk about evolution of GC, but only about its generating. [Generated, not degenerated code!] It makes sense to talk about the evolution of the genetic code only from the "moment" when the resulting peptide and nucleotide chains enter into chemical reactions and interactions; although even then it can be said that this is just a second phase of GC generation.

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